This study involved an assessment of the levels of microplastic pollution in seven small-scale estuaries in Shanghai for the first time. The abundance of microplastics ranged from 13.53 ± 4.6 to 44.93 ± 9.41 particles L−1, with a mean abundance of 27.84 ± 11.81 particles L−1. Microplastics collected from samples were classified into four types (fiber, film, granule, and fragment), and granules were the most abundant type. Up to 99.5% of microplastics were <2 mm in diameter. The microplastics had a variety of colors, with black being the dominant color. Polypropylene (37.5%) and polyethylene (50%) were the main types of microplastic component validated. Our study showed severe microplastic pollution in small-scale estuaries, and the associated rivers need urgent attention for microplastic pollution prevention. Display omitted •The high microplastic abundances were found in small-scale estuaries of Shanghai.•Granular, black and diminutive were the main features of the found microplastics.•Management strategies over microplastics were put forward for Chinese contexts.